Freesurfer

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30090 discussions

glmfit_sim for CVS mapped data
by Magnús Ingvi 07 Jul '17

07 Jul '17

Hi, I've been trying to run glmfit_sim on a glm analysis with data in the AVG_35_CVS space but it doesn't seem to finish (tried almost two weeks). Does anyone have an idea what might be going on here? I used mc_full for 1000 iterations for my simlation.

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Re: [Freesurfer] WM surface ignoring wm.mgz edits
by KALEY E ELLIS 07 Jul '17

07 Jul '17

Hi Bruce, We are using the "voxel-edit" tool and "recon editing" is selected. Thank you, Kaley ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Friday, July 7, 2017 11:00 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 161, Issue 16 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ---------------------------------------------------------------------- Message: 1 Date: Fri, 7 Jul 2017 10:42:23 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] WM surface ignoring wm.mgz edits To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1707071041590.9265(a)door.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="iso-8859-15" Hi Kaley are you using the "recon edit" tool in freeview? cheers Bruce On Fri, 7 Jul 2017, KALEY E ELLIS wrote: > > Dear?FreeSurfer?Developers, > > > We are attempting to make manual white matter edits to our subjects. The > edits are saving; however, after running with recon-all, the WM surface does > not appear to be taking into account our edits made to wm.mgz. Below is > additional information, and I have attached our recon-all.log. We are only > editing the cross because our dataset is comprised of single timepoints. > > > We are using?FreeSurfer?v5.3 and our operating system is OS X El?Capitan > version 10.11.6. > > Command to open and edit WM:? > > freeview -v mri/T1.mgz mri/brainmask.mgz mri/wm.mgz:opacity=0.5 -f > surf/lh.white:edgecolor=yellow surf/lh.pial:edgecolor=red > surf/rh.white:edgecolor=yellow surf/rh.pial:edgecolor=red > > > Command to submit edits: > > recon-all -autorecon2-wm -autorecon3 -subjid? > > > Recon-all log (see attached) > > > Thank you, > > Kaley?Ellis > > > > Associate Research Specialist > Center for?Healthy Minds > Waisman Center for Brain Imaging and Behavior > University of Wisconsin-Madison > > ------------------------------ Message: 2 Date: Fri, 7 Jul 2017 14:51:53 +0000 From: "Boyd, Emma" <EBOYD2(a)mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all on newborn To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <MWHPR04MB0558426F0D765C043BEDCABAD1AA0(a)MWHPR04MB0558.namprd04.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Hi Sarbani, Please see this paper for more information: https://www.ncbi.nlm.nih.gov/pubmed/25741260 A FreeSurfer-compliant consistent manual segmentation of ...<https://www.ncbi.nlm.nih.gov/pubmed/25741260> www.ncbi.nlm.nih.gov 1. Front Hum Neurosci. 2015 Feb 18;9:21. doi: 10.3389/fnhum.2015.00021. eCollection 2015. A FreeSurfer-compliant consistent manual segmentation of infant ... Emma ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Das S. <Sarbani.Das(a)soton.ac.uk> Sent: Friday, July 7, 2017 4:58:39 AM To: Freesurfer support list Subject: Re: [Freesurfer] recon-all on newborn Is there any paper that you can share that can explain why recon-all is not suitable for neonates brain apart from atlas. Sarbani -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Lilla Zollei Sent: 06 July 2017 21:43 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all on newborn It is not only the atlas but the tools that are different. Lilla On Wed, 5 Jul 2017, Das S. wrote: > Dear Lilla, > In that case you mean if I have my own atlas specific to neonates then I can follow these steps of auto recon. > If you give me little more details will be easy for me to understand the gap. > many thanks > Sarbani > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Lilla Zollei > [lzollei(a)nmr.mgh.harvard.edu] > Sent: 05 July 2017 22:32 > To: Freesurfer support list > Subject: Re: [Freesurfer] recon-all on newborn > > We use a similar pipeline but with different atlases and processing > steps for the newborns. > Lilla > > On Wed, 5 Jul 2017, Das S. wrote: > >> >> Thanks for the reply. If you let me know, among the below list of steps of current recon-all, currently which is not suitable to perform on neonates MRI image, will really appreciate. >> >> Autorecon Processing Stages: >> Motion Correction and Conform >> NU (Non-Uniform intensity normalization) >> Talairach transform computation >> Intensity Normalization 1 >> Skull Strip >> EM Register (linear volumetric registration) >> CA Intensity Normalization >> CA Non-linear Volumetric Registration >> Remove Neck >> LTA with Skull >> CA Label (Volumetric Labeling, ie Aseg) and Statistics >> Intensity Normalization 2 (start here for control points) >> White matter segmentation >> Edit WM With ASeg >> Fill (start here for wm edits) >> Tessellation (begins per-hemisphere operations) >> Smooth1 >> Inflate1 >> QSphere >> Automatic Topology Fixer >> Final Surfs (start here for brain edits for pial surf) >> Smooth2 >> Inflate2 >> Spherical Mapping >> Spherical Registration >> Spherical Registration, Contralateral hemisphere >> Map average curvature to subject >> Cortical Parcellation - Desikan_Killiany and Christophe (Labeling) >> Cortical Parcellation Statistics >> Cortical Ribbon Mask >> Cortical Parcellation mapping to Aseg >> >> BW >> S Das >> ________________________________________ >> From: freesurfer-bounces(a)nmr.mgh.harvard.edu >> [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Lilla Zollei >> [lzollei(a)nmr.mgh.harvard.edu] >> Sent: 04 July 2017 22:04 >> To: Freesurfer support list >> Subject: Re: [Freesurfer] recon-all on newborn >> >> Hi S Das, >> >> We are trying to release the infant pipeline by the end of the summer. >> >> Lilla >> >> On Tue, 4 Jul 2017, Das S. wrote: >> >>> Dear Freesurfer expert, >>> I want to perform recon-all pipeline on neonates data.Can I do so? >>> I was going through some mail archives and there it is said that on T1 image of neonates data we can't perform recon-all. >>> But again there is another paper where it says Freesurfer can perform segmentation of neonates image. >>> Any input will be appreciated. >>> Thanks >>> S Das >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to >> whom it is addressed. If you believe this e-mail was sent to you in >> error and the e-mail contains patient information, please contact the >> Partners Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to >> you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] wm.mgz in the internal structures
by Karla Rivera Figueroa 07 Jul '17

07 Jul '17

Thank you for the clarification. Have a nice weekend, Karla On Jul 7, 2017 10:16 AM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: Hi Karla you shouldn't have to worry about the wm.mgz in those regions if the aseg is accurate. cheers Bruce On Fri, 7 Jul 2017, Karla Rivera Figueroa wrote: Hi all, Do you need to edit the wm mask where the internal structures shown > in the aseg are? are the structures supposed to be covered entirely with > the > wm mask? > > Karla > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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WM surface ignoring wm.mgz edits
by KALEY E ELLIS 07 Jul '17

07 Jul '17

Dear FreeSurfer Developers, We are attempting to make manual white matter edits to our subjects. The edits are saving; however, after running with recon-all, the WM surface does not appear to be taking into account our edits made to wm.mgz. Below is additional information, and I have attached our recon-all.log. We are only editing the cross because our dataset is comprised of single timepoints. We are using FreeSurfer v5.3 and our operating system is OS X El Capitan version 10.11.6. Command to open and edit WM: freeview -v mri/T1.mgz mri/brainmask.mgz mri/wm.mgz:opacity=0.5 -f surf/lh.white:edgecolor=yellow surf/lh.pial:edgecolor=red surf/rh.white:edgecolor=yellow surf/rh.pial:edgecolor=red Command to submit edits: recon-all -autorecon2-wm -autorecon3 -subjid Recon-all log (see attached) Thank you, Kaley Ellis Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison

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wm.mgz in the internal structures
by Karla Rivera Figueroa 07 Jul '17

07 Jul '17

Hi all, Do you need to edit the wm mask where the internal structures shown in the aseg are? are the structures supposed to be covered entirely with the wm mask? Karla

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Matlab Problem LME
by Clara Kühn 07 Jul '17

07 Jul '17

Dear FreeSurfer experts, I am following the LME tutorial for the spatiotemporal mass-univariate model on Matlab 8.2. When I get to the point where the covariance estimates are segmented into homogeneous regions I run into a problem. Nothing really happens in Matlab anymore. This is my command: [lhRgs,lhRgMeans] = lme_mass_RgGrow (lhsphere, lhRe, lhTh0, lhcortex, 2, 95); And this is what the Matlab output looks like: connected to 12 workers. Starting region growing algorithm Computing seeds ... I've tried this already last week and nothing happened for a few days. When I terminate the command this is the Matlab output: Operation terminated by user during kron (after line 36) In lme_mass_RgGrow>homogenity (line 299) if (sum(sum(DistRgParams <= kron(ones(1,nv),thr),1) == np) >= prc*nv/100) &&... In lme_mass_RgGrow>merge (line 320) if homogenity(Re,Params,auxRgs,Rkn,nst,prc) In lme_mass_RgGrow>split (line 269) [Rgs,mrg] = merge(Rgs,Re,Params,mrgRgs(i),mrgRgs(j),nst,prc); In lme_mass_RgGrow>seeds (line 208) [Rgs,spltf(i),nnRgs] = split(Rgs,Re,Params,coord,splRgs(i),nst,prc); In lme_mass_RgGrow>vtxwGrowing (line 77) [Rgs1,Rgseed,Rgstd]= seeds(Re(:,maskvtx),Params(:,maskvtx),coord(:,maskvtx),nst,prc); In lme_mass_RgGrow (line 62) Regions = vtxwGrowing(Re,Theta,sphcoord,AdjM,maskvtx,nst,prc); I have then copied the function and added a few "fprintf" (see attachment) to get an idea as to where matlab has problems and the output looks like this: Starting region growing algorithm Computing seeds ... point5 point6 point7 point8 point7 point8 point7 point8 point7 point8 point7 point8 point7 point8 point7 point6 point7 point8 point7 point8 point7 point8 point7 point8 point7 point8 point7 [...] If I understand that correctly, matlab gets hung up on functions 'function tf = homogenity(Re,Params,Rgs,Rn,nst,prc)' and 'function [Rgs,tf] = merge(Rgs,Re,Params,Rn1,Rn2,nst,prc)'. Does anybody have an idea what that means and how it can be fixed? How long is this step supposed to take? I have 81 subjects with 1 - 3 time points. Any help or suggestions would be much appreciated! Cheers Clara -- Clara Kühn, Phd Candidate Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

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bbregister vs spmregister vs mri_coreg
by John Anderson 06 Jul '17

06 Jul '17

Dear Freesurfer experts, I see that the tool "mri_coreg" has been implemented recently in Free Surfer 6 and I really wanted to know what are the differences between the registration tools "bbregister", " spmregister" and "mri_coreg"! Kindly: 1. Are these tools similar? if not what are the differences ? 2. Is there any preference of using a tool over the others for specific type of data. For example: A. If I want to register FA map to T1 image which tool is more robust? B. if I want to register FA map to MNI space which tool is more robust? I highly appreciate your input on this! John

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Raw Cortical thickness values
by Muhammad Naveed Iqbal Qureshi 06 Jul '17

06 Jul '17

Dear Community, I need to know how can I read the numeric cortical thickness values from freesurfer processed files. (as there are too many in the surf folder) Thank you. Best Regards Naveed

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Average myelination within ROI
by SHAHIN NASR 06 Jul '17

06 Jul '17

Hi Surfers, I want to measure the average amount of myelinations within my ROI(s), I have already generated my myelination maps on surfaces (e.g. lh.myelin_ProjFrac0p5.nii ). Then I used mri_segstats as below: mri_segstats --i lh.myelin_ProjFrac0p5.nii --slabel SBJ_001 lh lh.V1 --sum V1_Stats.txt --accumulate but the numbers don't make any sense. For instance: # ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 125261 82573.4 Seg0000 110280.4453 0.2922 -5.5000 51.0000 56.5000 2 1 1138 764.8 Seg0001 941.0988 0.1572 0.2675 1.4203 1.1527 How can mean=941.0988 when the max=1.4203 ??? Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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Re: [Freesurfer] Still confused by group analysis..
by Douglas Greve 06 Jul '17

06 Jul '17

On 6/12/13 7:03 AM, Tudor Popescu wrote: > > Sorry Doug, wasn't sure whether you'd seen my last reply to this.. > > On 6 Jun 2013 21:37, "Tudor Popescu" <tudor3(a)gmail.com > <mailto:tudor3@gmail.com>> wrote: > > Thanks Doug, > > > > So if I want to use the study-specific "average" subject > surface with mri_surf2surf, rather than the generic > "fsaverage" one, how can this be done given that the > required ls.white file only exists in the latter but not > in the former? Can I just rename (or duplicate) ls.white > into ls.white_avg? > > You can copy it or create a symbolic link. > > So it is OK to copy the required lh.white file from the generic > average subject "fsaverage" and apply mri_surf2surf upon the > study-specific average subject ("average")? It still seems to me > that "average" should have its own (different) lh.white... > Yes it should. Did make_average_subject not create it? > > > > Shouldn't the input to mri_glmfit be the output of > mri_surf2surf? In the group tutorial, the former is > "lh.gender_age.thickness.10.mgh" while the latter is > "lh.gender_age.thickness.10B.mgh". Or should it just be > the unsmoothed output of mris_preproc? > > Yes, I can't remember why I put the "B" there, maybe to keep > people from overwriting lh.gender_age.thickness.10.mgh during > the tutorial and having to wait the 10min or so for it to get > recreated. > > But if all these commands transform the same file (output of > mris_preproc becomes input of mri_surf2surf, which then feeds into > mri_glmfit), then why is it still necessary to keep intact the > original lh.gender_age.thickness.10.mgh, when all you need for the > group analysis is the mri_surf2surf'd version? > Sorry, I'm lost here. What are the names of the files? > > > > Assuming the label files (corresponding to my ROI, and > extracted from the Destrieux atlas) are different for each > subject, and given mri_glmfit is called just once, for all > subjects, which label file (corresponding to what subject) > should I point it to? > > You need to create the label in the average subject. There is > a Destrieux atlas there. > > Again, by "average subject" do you mean here the generic one > (fsaverage) or the study-specific one (average)? Should the former > be used at any point of a group analysis, if the latter exists? > If you are doing your group analysis on a custom average, then do not use fsaverage at any point. doug

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